Sp110, a polypeptide component of the nuclear body

ABSTRACT

Cloning and characterization of a full length cDNA encoding Sp110 (speckled 110), a novel 110 kDa polypeptide, is disclosed. It is disclosed that Sp110 is a component of the nuclear body, is expressed in leukocytes, and is also expressed in other types of cells, including endothelial cells, smooth muscle cells, liver cells and heart cells, after contact with certain cytokines. The disclosure also includes the following: Sp140 recruits Sp110 to the nuclear body, Sp110 functions as an activator of gene transcription, and Sp110 serves as a nuclear hormone receptor co-activator. Sp110 DNAs, polypeptides, antibodies are disclosed. Also disclosed are Sp110-related screening methods and clinical diagnostic methods.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a national phase application under 35 U.S.C. Section 371 filed from International Patent Application PCT/US01/23248, filed 24 Jul. 2001, which claims priority to U.S. provisional patent application Ser. No. 60/220,305, filed 24 Jul. 2000. The contents of these applications are incorporated herein by reference in their entirety.

FEDERALLY SPONSORED RESEARCH

Work on the invention was supported in part by National Institutes of Health grants AR-01866 and DK-051179. Therefore, the government has certain rights in the invention.

TECHNICAL FIELD

This invention relates to molecular biology, biochemistry, cell biology, medicine and medical diagnostics.

BACKGROUND

The nuclear body is a multiprotein complex located within the nuclei of cells. The nuclear body is also known as nuclear domain 10, PML oncogenic domain, and the Kr body. Immunohistochemical staining typically indicates 5–30 nuclear bodies within a nucleus. The nuclear bodies appear as discrete, punctate regions. The number of nuclear bodies in the cell, and the intensity of antibody staining of these structures, increase in response to heat shock and viral infection, as well as following exposure to interferons and heavy metals (Ascoli et al., J. Cell Biol. 112:785–795, 1991). The nuclear body appears to be involved in the regulation of gene transcription. Nascent RNA polymerase II transcripts have been found within the nuclear body (LaMorte et al., Proc. Natl. Acad. Sci. USA 95:4991–4996, 1998), and the nuclear body is a preferred site for transcription of viral genes (Ishov et al., J. Cell. Biol. 138:5–16, 1997).

Promyelocytic leukemia (PML) protein is a component of the nuclear body. PML protein is involved in several cellular processes. For example, PML protein regulates cell growth (Wang, et al., Science 279:1547–1551, 1998) and may mediate apoptosis (Wang, et al., Nature Genetics 20:266–272, 1998; Quignon et al., Nature Genetics 10:259–265, 1998). PML protein also recruits cAMP response element-binding protein (the CREB-binding protein or CBP) to the nuclear body and functions as a potent nuclear hormone receptor co-activator (Doucas et al., Proc. Natl. Acad. Sci. USA 96:2627–2632, 1999).

In addition to its involvement in gene transcription, the nuclear body is a target of autoantibodies in the sera of patients who have primary biliary cirrhosis (P BC), an autoimmune disease (Hodges et al., Am. J. Hum. Genet. 63:297–304, 199&; Melnick et al., Blood 93: 3167–3215, 1999; Stemsdorf et al., Immunobiology 198:307–331, 1997). PBC patients carry autoantibodies directed against Sp100 (Speckled 100 kDa), a polypeptide component of the nuclear body (Szostecki et al., J. Immunol. 145:4338–4347, 1990). Two splice variants of Sp100, designated Sp100b and Sp100-HMG, have also been found (Dent et al., Blood 88:1423–1436, 1996; Seeler et al. Proc. Natl. Acad. Sci. USA. 95:7316–7321, 1998; Lehining et al., Proc. Natl. Acad. Sci. USA 95:7322–7326, 1998). These proteins interact with members of the heterochromatin protein 1 (HP1) family of non-histone chromosomal proteins. When bound to a promoter, the Sp100 proteins and HP1 behave as transcriptional repressors in transfected cells. These observations suggest that the nuclear body in general, and the Sp100 proteins in particular, may maintain chromatin architecture and regulate gene transcription (Seeler, et al. Proc. Natl. Acad. Sci. USA 95:7316–7321, 1998 and Lehming et al., Proc. Natl. Acad. Sci. USA 95:7322–7326).

Sera from PBC patients have also been used to identify a leukocyte-specific component of the nuclear body designated Sp140 (Bloch et al., J. Biol. Chem. 46:29198–29204, 1996). The N-terminal portion of Sp140 exhibits sequence homology with the N-terminal segments of the Sp100 proteins. The middle region of Sp140 contains a “SAND” domain (Gibson et al., Trends Biochem. Sci. 23:242–244, 1998), and the C-terminal portion of Sp140 contains a plant homeobox domain and a bromodomain.

SUMMARY

A full length cDNA encoding Sp110 Speckled 110), a novel 110 kDa polypeptide, has been discovered and characterized. It has been discovered that Sp110 is a component of the nuclear body, is expressed in leukocytes, and is also expressed in other types of cells, including endothelial cells, smooth muscle cells, liver cells and heart cells, after contact with, cytokines, including tumor necrosis factor, interleukin 1, and interferons. Other discoveries include the following: Sp140 recruits Sp110 to the nuclear body, Sp110 functions as an activator of gene transcription, and Sp110 serves as a nuclear hormone receptor co-activator.

Based on these and other discoveries, the invention features an isolated DNA containing a nucleotide sequence whose complement hybridizes under stringent hybridization conditions to a DNA molecule whose nucleotide sequence consists of nucleotides 405 to 797 of the Sp110 cDNA (SEQ ID NO:1). In some embodiments, the isolated DNA also includes at least one of the following: a nucleotide sequence encoding a domain having at least 80% sequence identity with amino acids 6–109 (Sp100-like domain) of the Sp110 polypeptide (SEQ ID NO:2); a domain having at least 80% sequence identity with amino acids 454–532 of SEQ ID NO:2 (SAND domain); a domain having at least 80% sequence identity with amino acids 537–577 of SEQ ID NO:2 (plant homeobox domain); and a domain having at least 80% sequence identity with amino acids 606–674 of SEQ ID NO:2 (bromodomain).

In some embodiments, the DNA hybridizes as described above and includes a nucleotide sequence encoding at least one of the following: amino acids 6–109 of SEQ ID NO:2 (Sp100-like domain) or amino acids 6–109 of SEQ ID NO:2 with one or more, e.g., 5, 10, 15 or 20 conservative amino acid substitutions therein; amino acids 454–532 of SEQ ID NO:2 (SAND domain) or amino acids 454–532 of SEQ ID NO:2 with one or more, e.g., 5, 10, 15 or 20, conservative amino acid substitutions therein; amino acids 537–577 of SEQ ID NO:2 (plant homeobox domain) or amino acids 537–577 of SEQ ID NO:2 with one or more, e.g., 5, 10, 15 or 20, conservative amino acid substitutions therein; and amino acids 606–674 of SEQ ID NO:2 (bromodomain) or amino acids 606–674 of SEQ ID NO:2 with one or more, 5, 10, 15 or 20, conservative amino acid substitutions therein.

In some embodiments, the isolated DNA hybridizes as described above, and also includes a nucleotide sequence encoding all of the following: amino acids 6–109 of SEQ ID NO:2 (Sp100-like domain) or amino acids 6–109 of SEQ ID NO:2 with one or more conservative amino acid substitutions therein; amino acids 454–532 of SEQ ID NO:2 (SAND domain) or amino acids 454–532 of SEQ ID NO:2 with one or more conservative amino acid substitutions therein; amino acids 537–577 of SEQ ID NO:2 (plant homeobox domain) or amino acids 537–577 of SEQ ID NO:2 with one or more conservative amino acid substitutions therein; and amino acids 606–674 of SEQ ID NO:2 (bromodomain) or amino acids 606–674 of SEQ ID NO:2 with one or more conservative amino acid substitutions therein.

In some embodiments, the isolated DNA contains a nucleotide sequence that encodes a polypeptide whose amino acid sequence is the sequence set forth as SEQ ID NO:2 or the sequence set forth as SEQ ID NO:2, with one or more, e.g., 5, 10, 15 or 20 conservative amino acid substitutions therein.

In some embodiments, the isolated DNA hybridizes as described above and also includes a nucleotide sequence encoding an Sp110 inhibitor polypeptide containing: amino acids 6–109 of SEQ ID NO:2 (Sp100-like domain) or amino acids 6–109 of SEQ ID NO:2 with one or more conservative amino acid substitutions therein; amino acids 537–577 of SEQ ID NO:2 (plant homeobox domain) or amino acids 537–577 of SEQ ID NO:2 with one or more conservative amino acid substitutions therein; and amino acids 606–674 of SEQ ID NO:2 (bromodomain) or amino acids 606–674 of SEQ ID NO:2 with one or more conservative amino acid substitutions therein; wherein the polypeptide does not contain a SAND domain.

In some embodiments, the isolated DNA contains a nucleotide sequence (Sp110 splice variant) that encodes the amino acid sequence set forth as SEQ ID NO:5, or the sequence set forth as SEQ ID NO:5 with one or more, e.g., 5, 10, 15 or 20, conservative amino acid substitutions therein.

The invention also features a vector containing any of the DNAs described above, and a host cell containing the vector. In the vector, the DNA can be operably linked to one or more expression control sequences.

The invention also features a substantially pure polypeptide encoded by any of the DNAs described above. In addition, the invention includes a substantially pure polypeptide (an inhibitor of Sp110 activity) containing an Sp110 Sp100-like domain, an Sp110 SAND domain, an Sp110 plant homeobox domain, and an Sp110 bromodomain, wherein the sequence of amino acids 110 to 453 of SEQ ID NO:2 is not present. In some embodiments, this polypeptide includes a membrane transport moiety, i.e., a moiety that allows the polypeptide to enter a cell. Exemplary membrane transport moieties are an internalization peptide sequence derived from Antennapedia and an HIV tat peptide.

The invention also features antibodies that bind specifically to the Sp110 polypeptide. The antibodies can be labeled.

The invention also features a screening method for identifying a compound that inhibits Sp110 dimerization. The method, which can be in vitro, includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate compound; and detecting a decrease in Sp110 dimerization in the presence of the candidate compound, as compared to Sp110 dimerization in the absence of the candidate compound.

The invention also features a screening method for identifying a compound that enhances or promotes Sp110 dimerization. The method, which can be in vitro, includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate compound; and detecting an increase in Sp110 dimerization in the presence of the candidate compound, as compared to Sp110 dimerization in the absence of the candidate compound.

The invention also features a screening method for identifying a polypeptide that dimerizes with Sp110 to form an inactive heterodimer. The method includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate polypeptide, thereby forming a test mixture; providing a gene expression system comprising a reporter gene operably linked to an Sp110-responsive expression control sequence; contacting the test mixture with the gene expression system; and detecting a decrease in reporter gene expression level in the presence of the test mixture, as compared to gene expression level in the presence of the Sp110 polypeptide sample solution. The gene expression system can be in a living cell, e.g., a transformed host cell. Alternatively, the gene expression system can be in vitro, i.e., acellular.

The invention also features a screening method for identifying a polypeptide that dimerizes with Sp110 to form a constitutively active or hyperactive heterodimer. The method includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate polypeptide, thereby forming a test mixture; providing a gene expression system comprising a reporter gene operably linked to an Sp110-responsive expression control sequence; contacting the test mixture with the gene expression system (which can be cellular or acellular); and detecting a constitutive activity or an increase in reporter gene expression level in the presence of the test mixture, as compared to gene expression level in the presence of the Sp110 polypeptide sample solution.

The invention also features a screening method for identifying a compound or polypeptide that inhibits Sp110 binding to a nuclear hormone receptor. The method, which can be in vitro, includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate compound; adding to the sample solution a nuclear hormone receptor; and detecting a decrease in Sp110 binding to the nuclear hormone receptor in the presence of the candidate compound, as compared to Sp110 binding to the nuclear hormone receptor in the absence of the candidate compound.

The invention also features a screening method for identifying a compound or polypeptide that enhances Sp110 binding to a nuclear hormone receptor. The method, which can be in vitro, includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate compound; adding to the sample solution a nuclear hormone receptor; and detecting an increase in Sp110 binding to the nuclear hormone receptor in the presence of the candidate compound, as compared to Sp110 binding to the nuclear hormone receptor in the absence of the candidate compound.

The invention also features a screening method for identifying a compound or polypeptide that inhibits the binding of an Sp110 dimer to an Sp110-binding nucleotide sequence. The method, which can be in vitro, includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate compound or polypeptide; adding to the sample solution an Sp110-binding nucleotide sequence; and detecting a decrease in Sp110 binding to the Sp110-binding nucleotide sequence in the presence of the candidate compound, as compared to Sp110 binding to the Sp110-binding nucleotide sequence in the absence of the candidate compound.

The invention also features a screening method for identifying a compound or polypeptide that enhances or promotes the binding of an Sp110 dimer to an Sp110-binding nucleotide sequence. The method, which can be in vitro, includes: providing an Sp110 polypeptide sample solution; adding to the sample solution a candidate compound or polypeptide; adding to the sample solution an Sp110-binding nucleotide sequence; and detecting an increase in Sp110 binding to the Sp110-binding nucleotide sequence in the presence of the candidate compound, as compared to Sp110 binding to the Sp110-binding nucleotide sequence in the absence of the candidate compound.

The invention also features a method for diagnosing primary biliary cirrhosis (PBC) in a human patient. The method includes: providing a substantially pure Sp110 polypeptide; providing a serum sample from the patient; contacting Sp110 polypeptide with the serum sample; and detecting specific binding of an antibody in the serum with the Sp110 polypeptide as an indication of PBC.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present application, including definitions, will control. All publications, patents and other references mentioned herein are incorporated by reference.

Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described below. The materials, methods and examples are illustrative only and not intended to be limiting. Other features and advantages of the invention will be apparent from the detailed description and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 is the nucleotide sequence of a full-length, human Sp110 cDNA (SEQ ID NO:1)

FIG. 2 is a comparison of the deduced amino acid sequences of Sp110 (SEQ ID NO:2) and Sp140 (SEQ ID NO:3). Shaded portions of the sequences indicate the Sp100-like domain, the SAND domain, the plant homeobox domain (PHD), and the bromodomain. Conserved cysteine/histidine residues within the PHD are marked with asterisks. A dashed box encloses a predicted nuclear localization sequence, and a solid box encloses the LXXLL-type nuclear hormone receptor interaction domain. The sequence of the interferon-inducible protein nuclear phosphoprotein 72 begins at amino acid-241 (met) and ends at amino acid 605 (leu), which are indicated by arrows.

FIG. 3 is the nucleotide sequence of the full-length, human Sp110 cDNA (SEQ ID NO:1) and the deduced amino acid sequence (reading frame c) of the Sp110 polypeptide (SEQ ID NO:2).

FIG. 4 is the nucleotide sequence of a human Sp110 splice variant cDNA (Sp110b) (SEQ ID NO:4) and the deduced amino acid sequence (reading frame c) of the Sp110b polypeptide (SEQ ID NO:5).

FIG. 5 is a schematic diagram comparing the domain structures of human Sp110, Sp140 and Sp100b. Also shown is the percent identity of the Sp110 domains, as compared to the corresponding domains in Sp140 and Sp100b.

DETAILED DESCRIPTION

The full-length, naturally-occurring, human Sp110 polypeptide includes an, Sp110-like domain (amino acids 6–109 of SEQ ID NO:2), a SAND domain (amino acids 454–532 of SEQ ID NO:2), a plant homeobox domain (PHD) (amino acids 537–577 of SEQ ID NO:2), and a bromodomain (amino acids 606–674 of SEQ ID NO:2). The full-length Sp110 functions as an activator of gene transcription. Sp110 also functions as a nuclear hormone receptor co-activator. Some embodiments of the invention include all of the domains in a single Sp110 polypeptide. In other embodiments, however, one or more of the domains is modified or absent.

The Sp100-like domain in the N-terminal portion of Sp110 has a potential helical motif, which can mediate homodimerization. (Seeler et al., Proc. Natl. Acad. Sci. USA 95:7316–7321, 1998). It is predicted that the Sp100-like domain in Sp110 functions in protein binding interactions, e.g., dimerization, with Sp140 or Sp100 to form a heterodimer, or dimerization with a second Sp110 polypeptide to form a homodimer. Therefore, a polypeptide that contains an Sp110 Sp100-like domain (or derivative thereof), but does not contain an activating domain, can be used in a cell to form inactive dimers comprising Sp140, Sp100 or Sp110. Such formation of inactive dimers reduces the availability of endogenous Sp140, Sp100 or Sp110 monomers for formation of active (transcription-activating or transcription-inhibiting) dimers, thereby reducing Sp140, Sp100, or Sp110 activity in the cell.

The Sp110 polypeptide is predicted to contain an activation domain located in the region between the Sp100-like domain and the SAND domain, i.e., in the region between amino acids 109 and 454 of SEQ ID NO:2. In some embodiments of the invention, a polypeptide containing this region or a derivative thereof is used to enhance or promote Sp110 activity.

Sp110 contains a SAND domain, variations of which are found in Sp100, Sp140, AIRE-1 (Nagamine et al., Nature Genetics 17:393–397, 1997), nuclear phosphoprotein 72, and DEAF-1 (Gross et al., EMBO J. 15:1961–1970, 1996). It is predicted that the Sp110 SAND domain is a DNA-binding domain (Gibson et al., Trends Biochem Sci. 23:242–244, 1998). In some embodiments of the invention, a polypeptide that contains a SAND domain (or derivative thereof), but lacks an activating domain, is employed as an inhibitor of Sp110 activity in a cell, e.g., a cell cultured in vitro. An example is an Sp110 polypeptide lacking the region extending from approximately amino acid 110 to amino acid 453 in SEQ ID NO:2. Such a polypeptide inhibits Sp110 activity because the SAND domain occupies some or all of the Sp110 binding sites, thereby blocking access of active Sp110 molecules to the binding sites. In some embodiments, a membrane transport moiety, e.g., the internalization peptide sequence derived from Antennapedia (Bonfanti et al., Cancer Res. 57:1442–1446) or an HIV tat peptide (U.S. Pat. No. 5,652,122) is conjugated to the SAND domain to facilitate entry of the SAND domain into living cells. In other embodiments, the carrier moiety is a polypeptide fused to the SAND domain or polypeptide containing the SAND domain, e.g., at the amino terminus of the SAND domain-containing polypeptide.

The full-length Sp110 polypeptide contains a plant homeobox domain (PHD). This is a cysteine-rich region that spans 50–80 amino acid residues and contains the motif Cys₄-His-Cys₃ (Aasland et al., Trends Biochem. Sci. 20:56–59, 1995). This motif is found in many proteins that are involved in chromatin-mediated control of gene transcription. It is predicted that the Sp110 PHD functions in protein-protein or protein-DNA interactions.

The full-length Sp110 polypeptide contains a bromodomain. It is predicted that the Sp110 bromodomain functions catalytically in acetylation of histones. The bromodomain is an α helical motif found in many proteins involved in the regulation of gene transcription (Jeanmougin et al., Trends Biochem. Sci. 22:151–153, 1997). In general, the bromodomain is found in transcription factors that have catalytic domains. For example, SW12/SNF2 has a DNA-dependent ATPase domain (Laurent et al., Genes Dev. 7:583–591, 1993), TAF_(II)250 (Dickstein et al., Cell 84:781–790, 1996) and TIF1α (Fraser et al., J. Biol. Chem. 273:16199–16204, 1998) have kinase domains, and GCN5 has a histone acetyl-transferase (HAT) domain (Brownwell et al., Cell 84:843–851, 1996). The original description of the bromodomain reported a conserved motif spanning approximately 60 amino acid residues and containing two a helices (Haynes et al., Nucl. Acids Res. 20;2603, 1992). Subsequently it has been suggested that the bromodomain spans 110 amino acid residues and contains two additional a helices (Le Douarin et al., EMBO J. 15:6701–6715, 1996). The four predicted a helices were designated Z, A, B, and C. The Sp110 bromodomain of SEQ ID NO:2 includes the A, B, and C helices but lacks the Z helix. Some Sp110 splice variants may have a Z helix.

Sp110 polypeptides, and fragments and derivatives thereof, can be obtained by any suitable method. For example, Sp110 polypeptides can be produced using conventional recombinant DNA technology, as described in the Examples below. Guidance and information concerning methods and materials for production of polypeptides using recombinant DNA technology can be found in numerous treatises and reference manuals. See, e.g., Sambrook et al, 1989, Molecular Cloning—A Laboratory Manual, 2^(nd) Ed., Cold Spring Harbor Press; Ausubel et al. (eds.), 1994, Current Protocols in Molecular Biology, John Wiley & Sons, Inc.; Innis et al. (eds.), 1990 PCR Protocols, Academic Press.

Alternatively, Sp110 polypeptides or fragments thereof can be obtained directly by chemical synthesis, e.g., using a commercial peptide synthesizer according to vendor's instructions. Methods and materials for chemical synthesis of polypeptides are well known in the art. See, e.g., Merrifield, 1963, “Solid Phase Synthesis,” J. Am. Chem. Soc. 83:21492154.

Percent identity between amino acid sequences referred to herein is determined using the BLAST 2.0 program, which is available to the public through the website for the National Center for Biotechnology Information. Sequence comparison is performed using an ungapped alignment and using the default parameters (Blossom 62 matrix, gap existence cost of 11, per residue gap cost of 1, and a lambda ratio of 0.85). The mathematical algorithm used in BLAST programs is described in Altschul et al., 1997, Nucleic Acids Research 25 :3389–3402.

As used herein “isolated DNA” means DNA that has been separated from DNA that flanks the DNA in the genome of the organism in the which the DNA naturally occurs. The term therefore includes a recombinant DNA incorporated into a vector, e.g., a cloning vector or an expression vector. The term also includes a molecule such as a cDNA, a genomic fragment, a fragment produced by PCR, or a restriction fragment. The term also includes a recombinant nucleotide sequence that is part of a hybrid gene construct, i.e., a gene construct encoding a fusion protein.

As used herein, “high stringency” means the following: hybridization at 42° C. in the presence of 50% formamide; a first wash at 65° C. with 2×SSC containing 1% SDS; followed by a second wash at 65° C. with 0.1×SSC.

As used herein, “substantially pure polypeptide” means a polypeptide separated from components that naturally accompany it. For example, a polypeptide is substantially pure when it is at least 80%, by weight, free from the proteins and other organic molecules with which it is naturally associated. Purity can be measured by any suitable method, e.g., column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis. A chemically synthesized polypeptide or a recombinant polypeptide produced in a cell type other than the cell type in which it naturally occurs is, by definition, substantially free from components that naturally accompany it.

As used herein, “conservative amino acid substitution” means a substitution within an amino acid family. Families of amino acid residues are recognized in the art and are based on physical and chemical properties of the amino acid side chains. Families include the following: amino acids with basic side chains (e.g. lysine, arginine, and histidine); amino acids with acidic side chains (e.g., aspartic acid and glutamic acid); amino acids with uncharged polar side chains (e.g. glycine, asparagine, glutamine, serine, threonine, tyrosine, and cysteine); amino acids with nonpolar side chains (e.g. alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, and tryptophan); amino acids with branched side chains (e.g., threonine, valine, and isoleucine); and amino acids with aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, and histidine). An amino acid can belong to more than one family.

A full-length Sp110 polypeptide, Sp110 polypeptide fragments containing individual Sp110 domains, or other antigenic Sp110 fragments, can be used to produce Sp110-specific antibodies. An example of an Sp110 fragment that can be used to elicit Sp110-specific antibodies is a polypeptide consisting of amino acids 219–235 of SEQ ID NO:2. The Sp110 specific antibodies can be readily obtained, without undue experimentation, through application of conventional techniques.

In view of its production by cells involved in host defense, i.e., leukocytes, and its induction by interferon (IFN) and cytokines, Sp110 appears to play a role in inhibiting viral replication and facilitating differentiation of cells, e.g., myeloid cells, and activation of cells involved in host defense. For example, an Sp110 polypeptide can be used therapeutically to treat myeloid malignancies by virtue of its ability to promote myeloid cell differentiation. In addition, the nuclear body, of which Sp110 is a structural component, is disrupted in various human disorders, including acute promyelocytic leukemia and viral infections. Therefore, in some embodiments of the invention, an Sp110 polypeptide (or derivative thereof) is introduced into a cell in vitro or in a mammal to enhance cellular defense mechanisms. In other embodiments, Sp110 is administered therapeutically to treat inflammation or to achieve alteration in lipid profiles.

A preformed Sp110 polypeptide can be introduced into a cell using conventional techniques for transporting proteins into intact cells, e.g., by fusing the polypeptide to the internalization peptide sequence derived from Antenntapedia (Bonfanti et al., Cancer Res. 57:1442–1446) or to an HIV tat peptide (U.S. Pat. No. 5,652,122). Alternatively, the Sp110 polypeptide can be expressed in the cell following introduction of an Sp110-encoding DNA, e.g., in a conventional expression vector, according to the invention. In some embodiments, Sp140 is concurrently introduced into the cell, or co-expressed in the cell, so that the Sp140 can recruit the Sp110 into nuclear bodies.

The biological activities of Sp110 include co-activation of nuclear hormone receptors, e.g., retinoic acid receptors (RARs), RXRs, LXR, FXR, peroxisome proliferator-activated receptors (PPARs), including PPARα and PPARγ, glucocorticoid receptors, estrogen receptors, progesterone receptors, androgen receptors, and orphan nuclear hormone receptors. Nuclear hormone receptors mediate signal transduction in various cellular responses. Sp110 appears to enhance expression of nuclear hormone-responsive genes by binding to a nucleotide sequence adjacent to the nuclear hormone response element and directly or indirectly enhancing gene expression. Activities of RARs and RXRs are important in cellular differentiation. Activities of PPARα and PPARγ are important in fatty acid metabolism and inflammation. Activities of FXR and LXR are important for cholesterol metabolism.

Where increased co-activation of an Sp110-responsive nuclear hormone receptor is needed, e.g., to enhance PPARα-mediated inhibition of the inflammatory response in smooth muscle cells or endothelial cells, an Sp110 polypeptide can be supplied in a therapeutic method. Similarly, in cardiac myocytes, Sp110 may augment PPARα's effect on lipid metabolism, potentially attenuating cardiac hypertrophy. Moreover, in adipocytes Sp110 may alter PPARγ regulation of lipid storage, potentially treating obesity.

Sometimes a nuclear hormone receptor-mediated response needs to be limited or reduced therapeutically. For example, an Sp110 derivative can be used to inhibit FXR receptors, thereby enhancing conversion of cholesterol to bile acids. In another example, Sp110 is used to block estrogen receptors in treatment of estrogen responsive tumors. The invention includes inhibitors of Sp110 activity, screening methods for identifying inhibitors of Sp110 activity, and methods of inhibiting Sp110 activity in, cells in vitro or in a mammal

Inhibition of Sp110 activity can be accomplished through approaches including the following: a polypeptide that dimerizes with endogenous Sp110 polypeptides to form an inactive dimer; a small molecule (MW=1000 Da or less) that interferes with Sp110 dimerization; a polypeptide that occupies Sp110 binding sites (nucleotide sequences) in DNA without causing transcriptional activation; and a small molecule that interferes with Sp110-nuclear hormone receptor interactions.

An example of a polypeptide predicted to dimerize with endogenous Sp110 polypeptides to form an inactive dimer is a polypeptide that includes amino acids 1–453 of the Sp110 sequence fused to amino acids 533–689 of the Sp110 sequence (amino acids 1–453 of SEQ ID NO:2 fused to amino acids 533–689 of SEQ ID NO:2). Such a polypeptide includes the entire Sp110 amino acid sequence except the Sp110 SAND domain, which is predicted to be required for recognizing and binding to Sp110 binding sites in DNA, but not required for Sp110 dimerization.

An example of a polypeptide predicted to recognize and occupy Sp110 binding sites (nucleotide sequences) in DNA without causing transcriptional activation is an Sp110 SAND domain or fragment thereof.

Polypeptides and other molecules, e.g., small molecules, that inhibit or promote Sp110 activity can be identified by screening methods provided by the invention. The type of screening method employed will depend on the type of inhibition mechanism chosen. One general approach is based on Sp110 dimerization, which is predicted to be necessary for Sp110 biological activity. One variation on this approach is to provide a molecule that interferes with Sp110 dimerization. Another variation on this approach is to provide a polypeptide that dimerizes with endogenous Sp110 polypeptides to form an inactive dimer. A second general approach is to provide a molecule that binds to (blocks) a site on the Sp110 polypeptide that interacts with nuclear hormone receptors. A third general approach is to interfere with binding of active Sp110 dimers to Sp110-binding DNA sequences in the genome. One variation on this approach is to provide a molecule, e.g., a polypeptide, that binds to (blocks) Sp110-binding DNA sequences. Another variation on this approach is to provide an oigonucleotide based on an Sp110-binding DNA sequence in the genome. The oligonucleotide binds to (blocks) the DNA-binding site(s) on the Sp110 dimer.

Primary biliary cirrhosis (PBC) is an autoimmune disease that predominantly affects intrahepatic bile ducts. As with many other autoimmune diseases, the vast majority of patients with PBC are women and the etiology of this disorder is unknown. The natural history of PBC is one of slowly progressive cholestasis with the development of cirrhosis and death unless the patient undergoes liver transplantation. Disease progression in an individual patient, however, is highly variable and a pre-symptomatic phase may last longer than 20 years (Springer et al., Am. J. Gastroenterol. 94:47–53,1999 and Mahl et al., J. Hepatol. 20:707–713, 1994). Because of the variable course of patients with PBC and the availability of novel treatments for this disease, it is important to identify prognostic factors that may distinguish those patients with mild disease (who may not require treatment) from those with a more aggressive, rapidly progressive, illness.

The invention provides methods for identifying and characterizing novel autoantibody markers of disease state and prognosis in PBC patients. Serum samples from PBC patients are tested for the presence of antibodies that react with Sp110. Various types of methods for detecting and quantifying such antibody-antigen reactions are known and can be employed.

In some embodiments of the invention, PBC-related autoantibodies are detected and characterized in methods such as conventional immunoblotting (Western) techniques, wherein an Sp110 polypeptide (or Sp110 polypeptide fragment) is employed as an antigen. Typically, the Sp110 polypeptide is subjected to SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and blotted (transferred) onto a suitable membrane, e.g., nitrocellulose, where the Sp110 antigen is immobilized. Sera from PBC patients are diluted as necessary and contacted with the Sp110 antigen-bearing membrane under suitable conditions for specific binding of the immobilized antigen to an anti-Sp110 antigen, if one is present. After suitable washing steps, bound antibody is detected.

Detection of bound antibody can be accomplished by any suitable method. For example, labeled protein A, which binds to IgG with high specificity and high affinity, can be used. The protein A can be labeled in any of various ways. Useful types of label include a conjugated calorimetric enzyme, e.g., horseradish peroxidase, a conjugated fluorochrome, e.g., FITC, or a radioactive atom, e.g., ¹²⁵I. Immunoblot assay results can be quantitated, for example, by incorporating internal standards and a suitable optical scanning device. Preferably, suitable positive and negative controls are employed in testing patient sera. In addition to Sp110, other nuclear body components such as Sp100, Sp140 polypeptides can be tested simultaneously, e.g., on the same immunoblot membrane.

In some embodiments of the invention, PBC-related autoantibodies are detected and quantitated using techniques designed for rapid, high-volume screening, e.g., microtiter plate ELISA techniques. Such techniques are known in the art and can be employed in practicing the present invention without undue experimentation.

EXAMPLES

The invention is farther illustrated by the following experimental examples. The examples are provided for illustrative purposes only, and are not to be construed as limiting the scope or content of the invention in any way.

Example 1 Isolation and Characterization of cDNA Clones Encoding Sp110

A nucleotide sequence in the EST database that encodes a polypeptide homologous to the N-terminal portions of Sp100 and Sp140 was obtained from the IMAGE consortium (accession number AA431918). This material proved unsuitable to prepare probes for screening a cDNA library because it was highly contaminated with unrelated cDNAs. Accordingly, two oligonucleotides were synthesized based upon the sequence of the EST clone (5′-TTGAATTCATGGAAGAGGCTCTTTTTCAG-3′ (SEQ ID NO:10) and 5′-TTGAATTCCTTCTGCTAGGCCAGTTGG-3′ (SEQ ID NO:11)) and the polymerase chain reaction (PCR) was used to synthesize a fragment of the cDNA. The PCR product was radiolabeled and used to screen a λGT10 cDNA library prepared from human spleen (Clontech, Palo Alto, Calif.). Six cDNA clones from among approximately one million bacteriophages hybridized with the radiolabeled probe and were isolated by plaque purification. Bacteriophage growth, DNA isolation, and subcloning into pUC19 were performed using standard procedures (Sambrook et al, 1989, Molecular Cloning—A Laboratory Manual, 2^(nd) Ed., Cold Spring Harbor Press, 1989). The nucleotide sequence of the full-length cDNA was determined by the dideoxy chain termination method (Sanger et al., Science 214:1205–1210, 1981). The sequences of the six clones, when assembled, revealed the sequence of the fall length Sp110 cDNA (FIG. 1).

The cDNA encoding Sp110 was 2,337 base pairs long, with an open reading frame from nucleotides 78 to 2144 encoding a protein containing 689 amino acids (FIGS. 1 and 3). The start codon was preceded by an in-frame stop codon, indicating that this is a full-length cDNA. The amino acid residues at 241 to 605 of Sp110 were essentially identical to residues 1 to 365 of a previously reported polypeptide designated nuclear phosphoprotein 72 (Kadereit et al., J. Biol. Chem. 268: 24432–24441, 1993). In this region, the amino acid sequence of Sp110 differed from that of nuclear phosphoprotein 72 at amino acid 580 (I-M).

The N-terminal portion of Sp110, between amino acid residues 6 and 159 was 49% identical to the N-terminal portions of both Sp100 (Szostecki et al., J. Immunol. 145:4338-4347, 1990) and Sp140 (Bloch et al., J. Biol. Chem. 46:29198–29204, 1996). A second region of homology between Sp110 and both Sp100b and Sp140 was present between amino acid residues 452 and 532. In this region, Sp110 was 53% identical to Sp100b (Dent et al., Blood 88:1423–1436, 1996) and 49% identical to Sp140. This portion of Sp100b and Sp140 was previously designated a SAND domain (Gibson et al., Trends Biochem Sci. 23:242–244, 1998). Sp110 amino acid residues 537 to 577 spanned a plant homeobox domain (Aasland et al., Trends Biochem. Sci. 20:56–59, 1995), and amino acid residues 606 to 674 contained the A, B, and C helices of a bromodomain (Jeanmougin et al., Trends Biochem Sci. 22:151–153, 1997). The plant homeobox domain and bromodomain of Sp110 were 71% and 54% identical to the corresponding regions in Sp140. In addition, these portions of Sp110 were 56% and 46% identical to the corresponding regions in murine TIF1α.

Example 2 Expression of Sp110 in Human Tissues and Cell Lines

The level of Sp110 mRNA in human tissues was determined by hybridizing membranes containing 2.5 μg of poly(A)⁺-selected RNA from human tissues (multiple tissue Northern blots, Clontech Laboratories, Palo Alto, Calif.) with a ³²P-radiolabeled 1.4 kb XbaI restriction fragment of the Sp110 cDNA. The human tissues represented on the membranes were spleen, thymus, prostate, testis, ovary, small intestine, colon, and peripheral blood leukocytes. The membranes were washed under stringent conditions and exposed to autoradiographic film for one hour. To confirm the presence of poly(A)⁺-selected RNA in each lane, the membranes were hybridized with a ³²P-radiolabeled β-actin cDNA probe. The membranes were washed under stringent conditions and exposed to autoradiography film for 30 minutes.

High levels of Sp110 mRNA were detected in human peripheral blood leukocytes and spleen. In contrast, lower levels of Sp110 mRNA were observed in thymus, prostate, testis, ovary, small intestine, and colon. In addition, low levels of Sp110 mRNA were observed in human heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas.

To investigate the expression of Sp110 in cells of the monocyte/granulocyte lineage, RNA was prepared from the myeloid precursor cell lines HL60 and NB4 (HL60 cells are available from the American Type Culture Collection, Manassas, Va.). RNA was extracted from these cell lines using the guanidinium isothiocyanate-cesium chloride method (Sambrook et al., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989). The HL60 cells were maintained in RPMI supplemented with 10% fetal calf serum, L-glutamine (2 mM), penicillin (200 units/ml), and streptomycin (200 mg/ml). RNA was fractionated in formaldehyde-agarose gels (5 μg/lane) and equal loading of RNA was confirmed by staining 28S and 18S ribosomal RNA with ethidium bromide. RNA was transferred to nylon membranes and the membranes were hybridized with the radiolabeled XbaI restriction fragment of the Sp110 cDNA or the EcoRI/BamHI restriction fragment of the cDNA encoding human Sp100 (Bloch et al., J. Biol. Chem. 46:29198–29204, 1996). Membranes were washed and analyzed by autoradiography. Low levels of Sp110 mRNA were detected in both NB4 cells and HL60 cells.

To examine the effect of cellular differentiation on Sp110 mRNA, NB4 cells were treated for 48 hours with all trans retinoic acid (ATRA) (1 μM). Following this treatment, the level of Sp110 mRNA was increased in NB4 cells, which indicates that differentiation of NB4 cells is associated with increased expression of Sp110. To examine the effect of IFN-γ treatment on Sp110 mRNA levels, HL60 cells were treated with IFN-γ (200 units/ml) for 48 hours. A marked increase in Sp110 mRNA was observed. These results demonstrated that, as with Sp100, PML, and Sp140, IFN-γ-treatment enhances expression of Sp110.

Sp110 expression was also examined in human coronary artery smooth muscle cells (hCASMCs) and human umbilical vein endothelial, cells (HUVECs) following exposure to IFNα (200 u/ml). Expression of Sp110 mRNA was induced within 4 hours and reached a maximum level between 8 and 24 hours. Similar results were obtained after treating hCASMCs or HUVECs with IFNγ or IL-1β and TNFα. Sp110 gene expression was also markedly induced in hearts of mice treated with endotoxin, suggesting that inflammatory mediators increase Sp110 mRNA levels in cardiac myocytes.

The observation that Sp110 was expressed in human leukocytes and cytokine-treated human vascular cells suggested that Sp110 is present in cells that have important roles in the pathogenesis of atherosclerosis.

Example 3 Cellular Localization of Sp110

To study the cellular location of Sp110, antiserum directed against a recombinant fragment of Sp110 (amino acid residues 219 to 324) was generated in rats, and an adenovirus vector encoding Sp110 (Ad.Sp110) was prepared.

To construct an E1-deleted, recombinant adenovirus vector containing Sp110, the cDNA encoding Sp110 was cloned into the NotI and BamHI sites of pAd.RSV₄, which contained the Rous sarcoma virus long-terminal repeat promoter and the SV40 polyadenylation signal. The plasmid containing Sp110 was co-transfected into 2093 cells with pSM17. Homologous recombination between the two plasmids resulted in an adenovirus (Ad.Sp110) that contained Sp110 sequences in place of E1 sequences. Recombinant viruses in a plaque were amplified in 293 cells, and a high-titer stock was prepared. The 293 cells were grown in low glucose (1 g/L)-DMEM supplemented with 10% horse serum. The absence of replication-competent adenovirus in the viral stock was confirmed by the failure of Ad.Sp110 to produce cytopathic changes in A549 lung carcinoma cells. In addition, PCR failed to amplify a DNA fragment corresponding to the E1 region of adenovirus using oligonucleotides and the Ad.Sp110 stock. An adenovirus vector containing the cDNA encoding Sp140 was described previously in (Bloch, et al., Mol. Cell. Biol. 19:4423–4430,1999).

To produce antibodies directed against Sp110, three male Sprague-Dawley rats were immunized with recombinant protein containing amino acid residues 219–435 of Sp110 fused to glutathione-S-transferase (GST). The plasmid encoding this portion of Sp110 was prepared by ligating a BstYI/EcoRV restriction fragment of the cDNA encoding Sp110 into the BamHI/SmaI sites of pGEX (Pharmacia Biotech, Inc., Piscataway, N.J.). The plasmid was used to transform E. coli, and expression of the fusion protein was induced by treatment with isopropyl-1-thio-β-D-galactopyranoside. The fusion protein was purified from E. coli proteins as described in (Smith et al., Gene 67:31–40, 1988). Primary immunizations of three rats was performed using 50 μg of purified protein emulsified in complete Freund's adjuvant for each animal. Two subsequent booster injections consisting of 50 μg of protein were given at two-week intervals.

The rat anti-Sp110 antiserum reacted with Sp110 in extracts prepared from Ad.Sp110-infected HEp-2 cells, but not with Sp140 in extracts prepared from Ad.Sp140-infected HEp-2 cells or with Sp100, which is normally expressed in HEp-2 cells. In contrast, rat anti-Sp140 antiserum, previously prepared against amino acid residues 131–391 of Sp140 (Bloch et al., J. Biol. Chem. 46:29198–29204, 1996), reacted with Sp140, but not with Sp110 or Sp100. These results demonstrated that the rat anti-Sp110 antiserum was specific for Sp110.

To investigate the cellular location of Sp110, rat anti-Sp110 antibodies were used to stain NB4 cells before and after treatment with RA. Anti-Sp110 antiserum stained nuclear bodies in NB4 cells that were treated for 48 hours with ATRA (1 μM), but did not react with untreated NB4 cells.

To determine the location of Sp110 with respect to the PML/Sp100 nuclear body, NB4 cells were treated with ATRA and stained with rat anti-Sp110 antiserum and human serum containing antibodies directed against Sp100. Sp110 co-localized with Sp100 in nuclear bodies.

To further investigate the cellular location of Sp110, adenovirus-mediated gene transfer was used to express Sp1110 in human cell lines in which it is not normally expressed. At a multiplicity of infection (MOI) of 25 viruses per cell, approximately 25% of HEp-2 cells expressed levels of Sp110 that were detectable by indirect immunofluorescence. Surprisingly, Sp110 did not localize to nuclear bodies in these cells, but instead appeared to produce a granular nuclear staining pattern with prominent staining near the nuclear membrane. Cytoplasmic staining was also observed in a few cells. The contrasting results obtained using the leukocyte cell line NB4 and Ad.Sp110-infected HEp-2 cells can be reconciled with the present result if Sp140, another leukocyte-specific nuclear body component, recruits Sp110 to the nuclear body. HEp-2 cells were infected with both Ad.Sp140, at an MOI of 50, and Ad.Sp110, at an MOI of 25. At an MOI of 50, essentially all of the HEp-2 cells expressed detectable Sp140 within nuclear bodies. In cells infected with Ad.Sp140 alone, anti-Sp110 antiserum did not stain nuclear bodies, confirming that anti-Sp110 antiserum did not cross-react with Sp140. In cells infected with both Sp110 and Sp140, Sp110 localized to nuclear bodies and co-localized with Sp100-containing nuclear bodies. These results demonstrated that Sp140 enhances localization of Sp110 to the nuclear body.

Example 4 Transcriptional Activation by Sp110

The amino acid sequence motifs in Sp110, including the SAND domain, the PHD, and the bromodomain, suggested that Sp110 has a role in the regulation of gene transcription. To examine the potential effect of Sp110 on gene transcription, a eukaryotic expression plasmid encoding Sp110 fused to the DNA-binding domain of GAL4 (pBXG-Sp1110) was co-transfected with a CAT reporter plasmid containing five GAL4 binding sites and an SV40 enhancer region (pG5SV-BCAT) into COS cells. There was a dose-dependent increase in CAT activity in cells transfected with increasing amounts of pBXG-Sp110. These results are similar to those observed using pBXG-Sp140 and different from those obtained with pBXG-Sp100. The GAL4-Sp100 fusion protein was previously shown to inhibit CAT activity when co-transfected with the reporter plasmid (Seeler et al. Proc. Natl. Acad. Sci. USA 95:73167321, 1998; Lehming et al., Proc. Nat. Acad. Sci. USA 95:7322–7326, 1998; and Bloch, et al., Mol. Cell. Biol. 19:4423–4430, 1999). These results demonstrated that Sp110 is capable of modulating gene transcription and acts in these cells as a transcriptional activator.

Experiments were also performed to determine whether Sp110 could function as a retinoic acid receptor (RAR) transcriptional co-activator. When co-transfected into COS cells with a reporter gene containing three copies of the RARα response element, Sp110 significantly enhanced ATRA-induced expression of the reporter gene. Similar results were observed in studies using HeLa cells instead of COS cells. The extent of reporter gene activation by Sp110 was similar to that induced by the nuclear body component PML. These results demonstrated that Sp110 can function as a co-activator of the nuclear hormone receptor RAR.

Sp110 also acted as a co-activator of PPARα. When COS cells were co-transfected with PPARα and a reporter gene containing three copies of the PPAR response element (PPRE), Sp110 markedly enhanced agonist-induced expression of the reporter gene compared with the effect of PPARα expressed alone. Sp110 may interact with nuclear hormone receptors via an LXXLL domain. To determine whether Sp110 interacts with PPARα via the LULL domain, oligonucleotides and PCR were used to prepare a mutant Sp110 protein (Sp110m) in which two of the three leucine residues were changed, one to valine and one to alanine (LXXVA).

Although immunoblot studies demonstrated that Sp110 and Sp110m were expressed at similar levels in transfected COS cells the Sp110 mutant activated the PPARα receptor less than wild-type Sp110. These results demonstrated that Sp110 functions as a PPARα transcriptional co-activator and indicated that the interaction between Sp110 and PPARα may involve the LXXLL nuclear hormone receptor interaction domain.

Sp110 enhanced signal transduction through the retinoic acid receptor α (RARα) (LaMorte et al., Proc Natl Acad Sci USA 95:4991–4996, 1998) and, in contrast to the results obtained with PPARα, expression of Sp110m with RARα also enhanced expression of the reporter gene. Similarly, both Sp110 and the Sp110 mutant enhanced signal transduction through the PPARγ receptor. These results suggested that Sp110 had an effect on RARα signaling and PPARγ signaling, perhaps through interaction with nucleotide motifs adjacent to nuclear hormone receptor response element(s). Although the examples below involved the PPARα receptor, it is predicted that similar results will be achieved with other nuclear hormone receptors.

Example 5 PPARα Interaction with CBP/p300

PPARα interacted with the N-terminal portion of CBP/p300 between amino acid residues 39 and 221. To determine whether Sp110 also interacts with CBP, the mammalian two-hybrid system was used as an assay. In this assay, the GAL4 DNA-binding domain (GAL4) fused to CBP (GAL4-CBP) and a luciferase reporter gene containing GAL4 response elements were expressed in COS cells with either Sp110 fused to the herpes simplex virus VP16 activation domain (VP16-Sp110) or VP16 alone. Expression of VP16-Sp110 significantly enhanced Ga14-CBP-induced luciferase gene activity compared with VP16 alone. Thus, Sp110 interacts, either directly or indirectly, with CBP. The site of functional interaction between Sp110 and CBP was mapped more specifically to amino acid residues 271–720 of CBP. The Sp110-CBP functional interaction domain is therefore distinct from the PPARα-CBP interaction domain.

To identify the portion of Sp110 that functionally interacts with CBP, the N-terminal or C-terminal portions of Sp110 were fused to VP16 and expressed in COS cells together with GAL4CBP and a reporter gene. The C-terminal portion, which contained the PHD and the bromodomain, enhanced GAL4-CBP-induced expression of the reporter gene, but the N-terminal portion, which contained the Sp100-like region, did not. As described below, studies can be carried out to further delineate the domains that mediate functional interaction between Sp110 and CBP and to test whether Sp110 interacts with CBP directly.

Sp110 does not contain motifs, such as acetyltransferase (as in CBP/p300) or kinase domains (as in TIF1α), that are known to activate gene transcription. To identify the portion of Sp110 that enhances reporter gene expression, DNA segments encoding fragments of Sp110 fused to GAL4 were expressed with a reporter gene in COS cells. Neither the N-terminal (Sp100-like domain), nor the C-terminal (PHD/bromodomain) portions of Sp110 increased expression of the reporter gene. In contrast, fusion proteins containing the middle portion of the protein (putative activation domain and SAND domain) increased reporter gene expression. The mechanism by which Sp110 enhances PPARα-mediated gene transcription can be investigated, as described below, by identifying proteins that interact with the activation domain and SAND domain.

Example 6 Sp110 and Expression of Genes Regulated by PPARα

This experiment tests the possibility that Sp110 enhances expression of a reporter gene under the control of the native promoter region of CPTI, a gene that is regulated by PPARα, Co-transfection studies are performed in COS cells using a luciferase reporter construct that contains a CPTI gene promoter having the PPRE (AGGGAAaAGGTCA; SEQ ID NO:12). The effect of co-expression of Sp110 and PPARα on luciferase activity is compared to that of Sp110, PPARα or control vectors alone. An expected result is that Spl 10 enhances PPARα mediated expression of the reporter gene under the control of the CPTI promoter region.

Sp110 may enhance luciferase expression by interacting with other regulatory elements within the CPTI promoter region. To demonstrate that the effect of Sp110 on luciferase activity requires PPARα, the effect of Sp110 on a luciferase reporter plasmid that has a mutated PPRE (AGGGAAaAccTCA; SEQ ID NO:13), is determined. If Sp110 enhances CPTI promoter-driven luciferase activity by interacting with PPARα, then an expected result is that Sp110 has no effect on expression of the reporter plasmid with the mutated PPRE.

Example 7 Sp110 and PPARα Cooperation in Mitochondrial Fatty Acid Oxidation Gene Expression

The fibroblast cell line 3T3-L1 can be induced to differentiate into cells that resemble white adipocytes. These cells normally express low levels of enzymes involved in mitochondrial fatty acid oxidation. To test the possibility that Sp110 enhances PPARα-mediated upregulation of mitochondrial fatty acid oxidation gene expression, Sp110 is overexptessed in 3T3-L1 cells using an adenovirus vector (Ad.Sp110). An unrelated protein, green fluorescent protein (GFP), is expressed as a control using a second adenovirus vector (Ad.GFP). 3T3-L1 cells will be infected with Ad.Sp110 or Ad.GFP at a virus MOI sufficient to produce infection of more than 90% of the cells. The cells are then incubated in medium containing insulin, 3-isobutyl-1-methylxanthine (IBMX), and dexamethasone to induce differentiation (Cao et al., Genes Dev., 5:1538–1552, 1991). Immunobloting is performed to confirm successful transgene expression. RNA blot hybridization will be performed to measure the effect of Sp110 (compared with GFP) on expression of three fatty acid oxidation genes (MCAD, LCAD, and CPT-I) in the presence or absence of the PPAR(X agonist WY 14,643.

To examine the effect of Sp110 on the rate of fatty acid oxidation, 3T3 L1 cells are infected with either Ad.Sp110 or Ad.GFP, and the rate of palmitate oxidation is determined (Gulick et al., Proc. Natl. Acad. Sci., USA, 91:11012–11016, 1994). Seventy-two hours after infection, the cells are incubated with [¹⁴C] palmitate. The tissue culture plates contain a central well with, a piece of filter paper. After 6 hours, the ¹⁴Co₂ is released from tissue culture medium by addition of 6 N HCl and ¹⁴CO₂ is collected overnight by alkalinization of the filter paper with 2 N NaOH. ¹⁴CO₂ is measured by scintillation counting of the filters.

Mutations in the LXXLL domain of Sp110 impair its ability to enhance PPARα-mediated expression of a reporter gene, most probably by blocking the direct interaction between PPARα and Sp110. To investigate the importance of the LXXLL domain in enhancing PPARα mediated gene expression, an adenovirus vector encoding Sp110m (Ad.Sp110m) is tested for its ability to induce expression of MCAD, LCAD, and CPT-I and to increase fatty acid oxidation in 3T3-L1 cells. The results of these tests with Ad.Sp110m are directly compared with those obtained using Ad.Sp110.

An expected result is that Sp110, but not GFP, enhances Wy 14,643-induced (PPARα agonist-induced) expression of genes involved in fatty acid oxidation and increase palmitate oxidation in 3T3-L1 cells. Because the effect of Sp110 on PPARα is expected to require direct interaction between the two proteins, Sp110 is expected to be more effective than Sp110m at producing these changes. If Sp110 and Sp110m are equally effective at inducing fatty acid oxidation, the putative LXXLL interaction domain in Sp110 is deemed non-crucial for this effect. In that event, studies to define alternative interaction sites between PPARα and Sp110 could be carried out.

3T3-L1 cells express relatively low levels of PPARα. In fact, these levels may be too low to detect any effect of Sp110 on genes normally regulated by PPARα. Thus, if there appears to be no enhancement of expression of genes involved in fatty acid oxidation following infection with Ad.Sp110, the studies are performed using an adenovirus vector encoding PPARα. Successful production of PPARα is confirmed using immunoblots and a commercially available anti-PPARα antibody. 3T3-L1 cells will be infected with Ad.GFP, Ad.Sp110, Ad.PPARα, or both Ad.Sp110 and Ad.PPARα. The effect of Ad.PPARα and Ad.Sp110 (together) on the expression of fatty acid oxidation genes and palmitate oxidation rates is compared to the effect of Ad.Sp110, Ad.PPARα, and Ad.GFP alone.

Example 8 Expression of Sp110 in hCASMCs and IL-1-Induced Production of IL-6 and Cyclooxygenase (COX)-2

Inflammatory cytokines such as IL-1 induce expression of IL-6 and COX-2 in smooth muscle cells (SMCs). This expression can be blocked, however, if the SMCs are; treated with PPARα agonists (Staels et al., J. Clin. Invest. 103:1489–1498, 1999). Endogenous Sp110 expression in SMCs was enhanced by treatment with inflammatory cytokines. Thus, Sp110 is expected to enhance PPARα-mediated inhibition of the inflammatory response in SMCs.

Forty-eight hours after human coronary artery SMCs (hCASMCs) are infected with Ad.Sp110, they are treated with recombinant human IL-1 and Wy14,643. The amount of IL-6 released by SMCs is measured by radioimmunoassay. To confirm that the effect of Ad.Sp110 on PPARα-mediated inhibition of IL-6 production is not a result of the Ad vector alone, control cells are infected, in parallel, with Ad.GFP at the same MOI as used for Ad.Sp110. Cells are treated with IL-1 and Wy14,643 and IL-6 production are measured as described above.

Because Sp110 also is expected to augment the ability of PPARα to inhibit COX-2 gene expression, SMCs are infected with Ad.Sp110 and subsequently treated with IL-I as described above. The cells are treated with increasing amounts of the PPARα agonist Wy14,643 and the concentration of COX-1 and COX-2 protein will be measured using immunoblot techniques. Parallel experiments are conducted with Ad.GFP as a control.

While the concentration of COX-1 is expected to be unaffected either by expression of Sp110 or by treatment with IL-1 or WY14,643, the concentration of COX-2 is expected to change. A lower concentration of COX-2 at each dose of WY14,643 in Ad.Sp110-infected cells (relative to Ad.GFP-infected cells), would suggest that Sp110 augments the ability of PPARα to inhibit COX-2 expression in SMCs in response to IL-I.

Example 9 Inhibiting PPARα-Sp110 Interaction in Cytokine-Treated hCASMCs

The biological function of Sp110 can be assessed in numerous ways, including studies in which it is overexpressed (as can be done to investigate its role in PPARα-mediated signal transduction) and studies in which oligopeptides are used as inhibitors (as can be done to inhibit the ligand-dependent interaction between PPARα and Sp110).

Two complementary oligonucleotides encoding a peptide that spans seven amino acids on either side of the LXXLL domain of Sp110 are synthesized and ligated, in frame, to GAL4 in a eukaryotic expression plasmid (pGAL-LXXL). To demonstrate that the GAL4-oligopeptide fusion protein acts an, inhibitor, this expression plasmid are co-transfected into COS cells with plasmids encoding PPARα, Sp110, and a reporter gene construct in which the reporter is driven by PPRE. As a control, cells are transfected in parallel with a plasmid encoding pGAL alone. The use of GAL4 as a fusion partner facilitates nuclear localization of the oligopeptide. In addition, successful production of the GAL4-oligopeptide fusion protein in transfection assays is confirmed by immunoblotting with anti-GAL4 antibodies. Expression of the GAL4-oligopeptide in COS cells is expected to block agonist-specific, Sp110-mediated, activation of PPARα.

To examine the effect of inhibiting the interaction between PPARα and Sp110 in hCASMCs, an adenovirus vector encoding GAL4-LXXLL and a control virus encoding GAL4 fused to the same amino acid residues in random rearrangement are prepared. hCASMCs are treated with IL-1 and subsequently infected with either Ad.GAL4-LXXLL or the control adenovirus vector. The production of IL-6 and the induction of COX-2 are assayed as described above.

Treatment of hCASMCs with cytokines induces expression of Sp110. Overexpression of an oligopeptide corresponding to the LXXLL domain in Sp110 would be expected to block Sp110 coactivation of PPARα-mediated gene expression. Thus, the oligopeptide is expected to enhance the cytokine-mediated induction of IL-6 and COX-2.

Example 10 Sp110 Interaction with PPARα

Mutations in the putative nuclear hormone receptor interaction domain of Sp110 inhibit the ability of Sp110 to enhance PPARα-mediated transcriptional activity. These results suggest that the LXXLL domain in Sp110 interacts with PPARα. It is possible, however, that other portions of Sp110 also mediate its interaction with PPARα. Mammalian two-hybrid assays are used to identify the portions of Sp110 and PPARα that mediate functional interaction between these two proteins.

To identify the portion(s) of Sp110 that mediate interaction with PPARα, DNA molecules encoding portions of Sp110 (the Sp100-like region, putative activation domain, SAND domain, LXXLL domain, PHD, and bromodomain, individually and in combination) are ligated into the eukaryotic expression vector pVP16 in-frame with the HSV VP16 activation domain. Each of the resulting plasmids are co-transfected into COS cells with a second plasmid encoding PPARα and a reporter gene containing a PPRE. Successful, production of each fragment of Sp110 is confirmed using immunoblots and an antibody directed against VP16. The ability of each VP16-Sp110 fusion protein to enhance reporter gene expression in the presence of PPARα and agonist provides evidence for a functional interaction between a given Sp110 portion and PPARα. Control experiments are conducted to rule out the possibility that VP16-Sp110 fusion proteins activate the reporter gene in the absence of PPARα. In addition, the inability of PPARα and VP16-Sp110 fusion proteins to activate reporter gene expression from a plasmid that lacks the PPRE will be confirmed.

To identify portions of PPARα that mediate interaction with Sp110, DNA molecules encoding portions of PPARα will be ligated into a eukaryotic expression plasmid in-frame with GAL4. The plasmids will be co-transfected with a plasmid encoding Sp110 fused to VP16 and a reporter gene with an upstream GAL4 response element. Gene expression mediated by GAL4-PPARα-fragment and Sp110 will be compared to that mediated by the same GAL4-PPARα-fragment and control plasmid. The ability of VP16-Sp110 to enhance GAL4-PPARα-fragment-induced reporter gene expression will be evidence of an interaction between Sp110 and a PPARα fragment.

These studies will identify the portions of Sp110 and PPARα that mediate functional interaction between the two proteins. Among others, the interaction domains should include the LXXLL domain of Sp110 and the ligand-binding “activation function 2” (AF2) portion of PPARα.

Example 11 Sp110 Direct Interaction with PPARα

Sp110 is predicted to interact directly with PPARα. A GST-Sp110 fusion protein is prepared and tested in vitro for interaction with ³⁵S-radiolabeled PPARA. DNA encoding Sp110 is ligated in-frame with DNA encoding glutathione-S-transferase (GST) in the prokaryotic expression plasmid pGEX so as to encode a GST-Sp110 fusion protein. The recombinant fusion protein is expressed in E. coli, affinity-purified, and immobilized on Sepharose beads. DNA encoding PPARα are used to prepare ³⁵S-radiolabeled protein by in vitro transcription and translation and will be incubated with Sepharose-GST-Sp110 (or Sepharose-GST alone) in the presence and absence of PPARα agonist. Bound and radiolabeled PPARα is eluted from Sepharose-GST-Sp110 (or Sepharose-GST) by boiling in SDS/PAGE sample buffer, and the eluant will be fractionated by SDS/PAGE.

Retention of PPARα on Sepharose-GST-Sp110, but not on control Sepharose-GST, provides evidence for a direct interaction between PPARα and Sp110. In addition, if PPARα is retained on Sepharose-GST-Sp110 in the presence, but not in the absence, of PPARα agonist then the direct interaction between PPARα and Sp110 requires the presence of nuclear hormone receptor agonist.

Example 12 Sp110 Interaction with CBP

A mammalian two-hybrid assay was used to demonstrate a functional interaction between the PHD/bromodomain of Sp110 and amino acids 271–720 of CBP. Sp110 may also interact directly with CBP. To determine whether or not it does, a GST-CBP (271–720) fusion protein will be prepared (as described above for Sp110) and exposed to ³⁵S-radiolabeled Sp110. An ³⁵S-radiolabeled nuclear body component, PML, can serve as a positive control for interaction with CBP, as PML interacts with CBP in this portion of the protein (Doucas et al., Proc. Natl. Acad. Sci. USA, 96:2627–2632, 1999). If CBP interacts directly with Sp110, then a Sepharose-GST-CBP (271–720) fusion protein, but not Sepharose-GST alone, would be expected to retain radiolabeled Sp110.

CBP has been described as a “platform” protein because it interacts with many other proteins. Among the proteins that interact with CBP at amino acid residues 271–720 are: RXR, STAT2, CREB, JUN, MYYB, ELK1, SREBP, and SAP1A (Giles et al., Trends Genetics, 14:178–183, 1998). Instead of a direct interaction between Sp110 and CBP, at least one other protein may mediate the functional interaction between these two proteins. If a direct interaction between Sp110 and CBP cannot be demonstrated using GST pulldown experiments, then the mammalian two-hybrid system will be used to further delineate the site in CBP that mediates functional interaction with Sp110. Two approaches can then be taken to identify the protein(s) that link CBP and Sp110. A candidate gene approach will involve obtaining cDNAs encoding proteins that are known to interact with the identified portion of CBP. Proteins encoded by these cDNAs will be tested for interaction with Sp110 using a combination of GST pull-down and mammalian two-hybrid assays. If none of the candidate genes interacts with Sp110, then the yeast two-hybrid system will be used to identify cDNAs encoding proteins that link CBP and Sp110. A DNA fragment encoding the PHD/bromodomain of Sp110, and a DNA fragment encoding the portion of CBP that mediates functional interaction with Sp110, will each be used to screen a human leukocyte cDNA library. Complementary DNAs encoding interacting proteins will be divided into groups that interact with Sp110, CBP, or both. Verification of “true” protein-protein interactions are then performed, as described below.

Example 13 Sp110 SAND Domain and Transcriptional Activation

Sp110 appears to enhance expression of nuclear hormone responsive genes by binding to a nucleotide sequence adjacent to the nuclear hormone response element and directly or indirectly enhancing gene expression. The sand domain of Sp110 may mediate DNA binding. By interacting directly with DNA, Sp110 may enhance gene expression independent of the LXXLL motif. A GAL4-Sp110 fusion protein is capable of activating expression of a reporter gene driven by the GAL4 response element, and neither the N-terminal, which contains the Sp100-like domain, nor the C-terminal, which contains the LXXLL/PHD/bromodomain) of Sp110 are required to mediate enhanced expression of the reporter gene. The middle portion of Sp110 contains a SAND domain, an amino acid sequence motif that has been observed in several proteins that regulate gene transcription.

To identify and characterize cDNAs encoding proteins that interact with Sp110's activation domain, a DNA fragment encoding that domain will be used as “bait” in the yeast two-hybrid assay. The DNA fragment are ligated into plasmid pGBKT7 (Clontech) and transferred into yeast with a leukocyte cDNA library prepared in pGADT7. The transformed yeast will be screened for the ability to grow on His⁻ medium and colonies that grow on this medium will be tested for α-galactosidase (α-gal) activity. Complementary DNAs are recovered from positive yeast clones and re-tested for interaction with bait by a second round of transformation in yeast. If numerous positive clones are obtained, they will be sorted into groups on the basis of size and restriction sites, and representative clones will be tested for interaction with an unrelated bait fusion protein. Clones encoding proteins that specifically interact with the Sp110 activation domain, but not the unrelated protein, will be sequenced and further characterized

In vitro co-immunoprecipitation, in vivo co-immunoprecipitation and mammalian two-hybrid assays will be used to confirm functional interactions between Sp110 and proteins produced by cDNAs identified using yeast two-hybrid. These studies identify cDNAs encoding proteins that interact with the activation domain of Sp110. The identity of these proteins will provide additional information regarding the mechanism by which Sp110 functions as a nuclear hormone receptor co-activator.

In an alternative approach, proteins that interact with the activation domain are identified by purifying interacting proteins from cell extracts using recombinant Sp110 protein linked to Sepharose beads. Purified proteins will be fractionated in polyacrylamide gels, transferred to IMMOBILON™ filters, and subjected to amino acid microsequencing. These techniques have been used previously to purify and identify the predominant autoantigen in patients with autoimmune sensorineural hearing loss (Bloch et al., Archives of Otolaryngology-Head and Neck Surgery 121:1167–1171, 1995).

Example 14 Sp110 in PBC Diagnosis

This study demonstrates that antibodies directed against nuclear body components Sp140 and Sp110 identify a subset of PBC patients with a variant form, e.g., a relatively mild form, of PBC. Serum from a well-defined cohort of 370 PBC patients are tested by immunoblot for antibodies directed against Sp110 and Sp140.

Adenovirus vectors containing cDNAs encoding Sp140, Sp110, and Sp100 produce high levels of protein in human 293 cells. Aliquots of cell lysates sufficient to screen 5,000 sera for each of these antigens are prepared. Cell lysates are boiled in loading buffer, fractionated in an 8% polyacrylamide gel, and transferred to nitrocellulose membranes. A miniblot apparatus is applied to the membrane. This permits screening of 20 sera on each membrane. As a preliminary screen, patient serum is diluted 1:200 in PBS containing 5% nonfat dry milk and incubated for one hour at room temperature with the nitrocellulose. Membranes are washed three times with PBS and incubated with horseradish peroxidase (HRP) conjugated-protein A diluted 1:5000 in PBS. Filters are washed three times in PBS, incubated with chemiluminescence reagent, and then exposed to film. If a serum sample appears to contain antibodies directed against the recombinant protein, then a second immunoblot is performed. This second membrane has two lanes, one containing protein from 293 cells infected with adenovirus encoding the nuclear body protein, and the second containing protein from cells infected with the control adenovirus. The presence of an appropriate size band in the former lane, but not the latter, is taken as confirmation of the presence of autoantibodies directed against the nuclear body component. This second immunoblot excludes false-positive results that may be secondary to human antibodies reacting with 293 cell proteins or adenovirus proteins produced in these cells.

The diagnosis of PBC in the 370-patient cohort is established based on the presence of abnormal liver function tests, AMA (titer≧1:20) and liver biopsy compatible with PBC. The findings on liver biopsy are classified into four stages (portal hepatitis, periportal hepatitis, septal fibrosis and/or bridging necrosis, cirrhosis). The cohort includes 234 women and 36 men. The date of presentation was defined as the first documentation of abnormal liver enzymes. The median age at presentation is 52 years (range 24–81). The median length of follow-up is nine years (range 1–27). Symptoms of PBC in these patients include pruritis, jaundice, portosystemic encephalopathy, bleeding varices, edema and ascites. Endpoints of the study are liver transplantation, death from liver disease and death from other causes.

To demonstrate that antibodies directed against Sp110 and Sp140 identify a subset of patients with a mild form of PBC, serum from these patients are screened for the presence of antibodies using immunoblot as described above. For the purpose of this study, mild disease is defined as liver biopsy at presentation showing stage I or II disease and survival during the course of the study without requiring liver transplantation.

Other Embodiments

A number of embodiments of the invention have been described. Nevertheless, it is understood that various modifications may be made without departing from the spirit and scope of the invention. Other embodiments are within the scope of the claims that follow. 

1. A substantially pure polypeptide comprising the amino acid sequence of SEQ ID NO:2.
 2. The polypeptide of claim 1, wherein the polypeptide consists of the amino acid sequence of SEQ ID NO:2.
 3. The polypeptide of claim 1, further comprising a membrane transport moiety.
 4. The polypeptide of claim 3, wherein the membrane transport moiety is selected from the group consisting of the internalization peptide sequence derived from Antennapedia and an HIV tat peptide.
 5. A substantially pure polypeptide consisting of the amino acid sequence of SEQ ID NO:2 and a membrane transport moiety.
 6. The polypeptide of claim 5, wherein the membrane transport moiety is selected from the group consisting of the internalization peptide sequence derived from Antennapedia and an HIV tat peptide.
 7. A substantially pure polypeptide comprising the amino acid sequence of SEQ ID NO:2 with one or more, but not more than 20, conservative amino acid substitutions therein.
 8. The polypeptide of claim 7, wherein the polypeptide comprises SEQ ID NO:2 with 5, 10, 15 or 20 conservative amino acid substitutions therein.
 9. The polypeptide of claim 8, further comprising a membrane transport moiety.
 10. The polypeptide of claim 9, wherein the membrane transport moiety is selected from the group consisting of the internalization peptide sequence derived from Antennapedia and an HIV tat peptide.
 11. A substantially pure polypeptide comprising an Sp110 Sp100-like domain (amino acids 6–109 of SEQ ID NO:2) and an Sp110 SAND domain (amino acids 454–532 of SEQ ID NO:2), but lacking the sequence of amino acids 110–453 of SEQ ID NO:2.
 12. The polypeptide of claim 11, wherein the polypeptide consists of an Sp110 Sp100-like domain (amino acids 6–109 of SEQ ID NO:2) and an Sp110 SAND domain (amino acids 454–532 of SEQ ID NO:2).
 13. A substantially pure polypeptide comprising an Sp110 Sp100-like domain (amino acids 6–109 of SEQ ID NO:2) and an Sp110 plant homeobox domain (amino acids 537–577 of SEQ ID NO:2), but lacking the sequence of amino acids 110–453 of SEQ ID NO:2.
 14. The polypeptide of claim 13, wherein the polypeptide consists of an Sp110 Sp100-like domain (amino acids 6–109 of SEQ ID NO:2) and an Sp110 plant homeobox domain (amino acids 537–577 of SEQ ID NO:2).
 15. A substantially pure polypeptide comprising an Sp110 Sp-100-like domain (amino acids 6–109 of SEQ ID NO:2), an Sp110 SAND domain (amino acids 454–532 of SEQ ID NO:2), an Sp110 plant homeobox domain (amino acids 537–577 of SEQ ID NO:2), and an Sp110 bromodomain (amino acids 606–674 of SEQ ID NO:2), wherein the sequence of amino acids 110 to 453 of SEQ ID NO:2 is not present.
 16. A substantially pure polypeptide consisting of an Sp110 Sp-100-like domain (amino acids 6–109 of SEQ ID NO:2), an Sp110 SAND domain (amino acids 454–532 of SEQ ID NO:2), an Sp110 plant homeobox domain (amino acids 537–577 of SEQ ID NO:2), and an Sp110 bromodomain (amino acids 606–674 of SEQ ID NO:2). 